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NASA NTRS2015

GeneLab: NASA's Open Access, Collaborative Platform for Systems Biology and Space Medicine

NASA is investing in GeneLab1 (http:genelab.nasa.gov), a multi-year effort to maximize utilization of the limited resources to conduct biological and medical research in space, principally aboard the International Space Station (ISS). High-throughput genomic, transcriptomic, proteomic or other omics analyses from experiments conducted on the ISS will be stored in the GeneLab Data Systems (GLDS), an open-science information system that will also include a biocomputation platform with collaborative science capabilities, to enable the discovery and validation of molecular networks.

Berrios, Daniel C.↗

NASA NTRS2015

GeneLab: NASA's Open Access, Collaborative Platform for Systems Biology and Space Medicine

Berrios, Daniel C.↗

NASA NTRS2002

An Extensible Schema-less Database Framework for Managing High-throughput Semi-Structured Documents

Object-Relational database management system is an integrated hybrid cooperative approach to combine the best practices of both the relational model utilizing SQL queries and the object oriented, semantic paradigm for supporting complex data creation. In this paper, a highly scalable, information on demand database framework, called NETMARK is introduced. NETMARK takes advantages of the Oracle 8i object-relational database using physical addresses data types for very efficient keyword searches of records for both context and content. NETMARK was originally developed in early 2000 as a research and development prototype to solve the vast amounts of unstructured and semi-structured documents existing within NASA enterprises. Today, NETMARK is a flexible, high throughput open database framework for managing, storing, and searching unstructured or semi structured arbitrary hierarchal models, XML and HTML.

Maluf, David A.↗

NASA NTRS2014

HEMODOSE: A Set of Multi-parameter Biodosimetry Tools

After the events of September 11, 2001 and recent events at the Fukushima reactors in Japan, there is an increasing concern of the occurrence of nuclear and radiological terrorism or accidents that may result in large casualty in densely populated areas. To guide medical personnel in their clinical decisions for effective medical management and treatment of the exposed individuals, biological markers are usually applied to examine the radiation induced changes at different biological levels. Among these the peripheral blood cell counts are widely used to assess the extent of radiation induced injury. This is due to the fact that hematopoietic system is the most vulnerable part of the human body to radiation damage. Particularly, the lymphocyte, granulocyte, and platelet cells are the most radiosensitive of the blood elements, and monitoring their changes after exposure is regarded as the most practical and best laboratory test to estimate radiation dose. The HEMODOSE web tools are built upon solid physiological and pathophysiological understanding of mammalian hematopoietic systems, and rigorous coarse-grained biomathematical modeling and validation. Using single or serial granulocyte, lymphocyte, leukocyte, or platelet counts after exposure, these tools can estimate absorbed doses of adult victims very rapidly and accurately. Some patient data in historical accidents are utilized as examples to demonstrate the capabilities of these tools as a rapid point-of-care diagnostic or centralized high-throughput assay system in a large scale radiological disaster scenario. Unlike previous dose prediction algorithms, the HEMODOSE web tools establish robust correlations between the absorbed doses and victim's various types of blood cell counts not only in the early time window (1 or 2 days), but also in very late phase (up to 4 weeks) after exposure

Hu, Shaowen↗

NASA NTRS2014

HEMODOSE: A Set of Multi-parameter Biodosimetry Tools

There continues to be important concerns of the possibility of the occurrence of acute radiation syndromes following nuclear and radiological terrorism or accidents that may result in mass casualties in densely populated areas. To guide medical personnel in their clinical decisions for effective medical management and treatment of the exposed individuals, biological markers are usually applied to examine radiation induced biological changes to assess the severity of radiation injury to sensitive organ systems. Among these the peripheral blood cell counts are widely used to assess the extent of radiation induced bone marrow (BM) injury. This is due to the fact that hematopoietic system is a vulnerable part of the human body to radiation damage. Particularly, the lymphocyte, granulocyte, and platelet cells are the most radiosensitive of the blood elements, and monitoring their changes after exposure is regarded as a practical and recommended laboratory test to estimate radiation dose and injury. In this work we describe the HEMODOSE web tools, which are built upon solid physiological and pathophysiological understanding of mammalian hematopoietic systems, and rigorous coarse-grained biomathematical modeling and validation. Using single or serial granulocyte, lymphocyte, leukocyte, or platelet counts after exposure, these tools can estimate absorbed doses of adult victims very rapidly and accurately to assess the severity of BM radiation injury. Some patient data from historical accidents are utilized as examples to demonstrate the capabilities of these tools as a rapid point-of-care diagnostic or centralized high-throughput assay system in a large-scale radiological disaster scenario. HEMODOSE web tools establish robust correlations between the absorbed doses and victim's various types of blood cell counts not only in the early time window (1 or 2 days), but also in very late phase (up to 4 weeks) after exposure.

Hu, Shaowen↗

NASA NTRS2014

A Multiple Parameters Biodosimetry Tool with Various Blood Cell Counts - the Hemodose Approach

There continue to be important concerns about the possibility of the occurrence of acute radiation syndromes following nuclear and radiological terrorism or accidents that may result in mass casualties in densely populated areas. To guide medical personnel in their clinical decisions for effective medical management and treatment of the exposed individuals, biological markers are usually applied to examine radiation induced biological changes to assess the severity of radiation injury to sensitive organ systems. Among these the peripheral blood cell counts are widely used to assess the extent of radiation induced bone marrow injury. This is due to the fact that the hematopoietic system is the most vulnerable part of the human body to radiation damage. Particularly, the lymphocyte, granulocyte, and platelet cells are the most radiosensitive of the blood elements, and monitoring their changes after exposure is regarded as a practical and recommended laboratory test to estimate radiation dose and injury. Based upon years of physiological and pathophysiological investigation of mammalian hematopoietic systems, and rigorous coarse-grained bio-mathematical modeling and validation on species from mouse, to dog, monkey, and human, we have developed a set of software tools Hemodose, which can use single or serial granulocyte, lymphocyte, leukocyte, or platelet counts after exposure to estimate absorbed doses of adult victims very rapidly and accurately. Some patient data from historical accidents are utilized as examples to demonstrate the capabilities of these tools as a rapid point-of-care diagnostic or centralized high-throughput assay system in a large-scale radiological disaster scenario. Most significant to the improvement of national and local preparedness of a potential nuclear/radiological disaster, this HemoDose approach establishes robust correlations between the absorbed doses and victim's various types of blood cell counts not only in the early time window (1 or 2 days), but also in the very late phase (up to 4 weeks) after exposure.

Hu, Shaowen↗

NASA NTRS1981

A low-power, high-throughput maximum-likelihood convolutional decoder chip for NASA's 30/20 GHz program

It is pointed out that the NASA 30/20 GHz program will place in geosynchronous orbit a technically advanced communication satellite which can process time-division multiple access (TDMA) information bursts with a data throughput in excess of 4 GBPS. To guarantee acceptable data quality during periods of signal attenuation it will be necessary to provide a significant forward error correction (FEC) capability. Convolutional decoding (utilizing the maximum-likelihood techniques) was identified as the most attractive FEC strategy. Design trade-offs regarding a maximum-likelihood convolutional decoder (MCD) in a single-chip CMOS implementation are discussed.

Mccallister, R. D.↗

NASA NTRS2011

IONAC-Lite

The Interplanetary Overlay Net - working Protocol Accelerator (IONAC) described previously in The Inter - planetary Overlay Networking Protocol Accelerator (NPO-45584), NASA Tech Briefs, Vol. 32, No. 10, (October 2008) p. 106 (http://www.techbriefs.com/component/ content/article/3317) provides functions that implement the Delay Tolerant Networking (DTN) bundle protocol. New missions that require high-speed downlink-only use of DTN can now be accommodated by the unidirectional IONAC-Lite to support high data rate downlink mission applications. Due to constrained energy resources, a conventional software implementation of the DTN protocol can provide only limited throughput for any given reasonable energy consumption rate. The IONAC-Lite DTN Protocol Accelerator is able to reduce this energy consumption by an order of magnitude and increase the throughput capability by two orders of magnitude. In addition, a conventional DTN implementation requires a bundle database with a considerable storage requirement. In very high downlink datarate missions such as near-Earth radar science missions, the storage space utilization needs to be maximized for science data and minimized for communications protocol-related storage needs. The IONAC-Lite DTN Protocol Accelerator is implemented in a reconfigurable hardware device to accomplish exactly what s needed for high-throughput DTN downlink-only scenarios. The following are salient features of the IONAC-Lite implementation: An implementation of the Bundle Protocol for an environment that requires a very high rate bundle egress data rate. The C&DH (command and data handling) subsystem is also expected to be very constrained so the interaction with the C&DH processor and the temporary storage are minimized. Fully pipelined design so that bundle processing database is not required. Implements a lookup table-based approach to eliminate multi-pass processing requirement imposed by the Bundle Protocol header s length field structure and the SDNV (self-delimiting numeric value) data field formatting. 8-bit parallel datapath to support high data-rate missions. Reduced resource utilization implementation for missions that do not require custody transfer features. There was no known implementation of the DTN protocol in a field programmable gate array (FPGA) device prior to the current implementation. The combination of energy and performance optimization that embodies this design makes the work novel.

Torgerson, Jordan L.↗

NASA NTRS1999

Modeling and Simulation Reliable Spacecraft On-Board Computing

The proposed project will investigate modeling and simulation-driven testing and fault tolerance schemes for Spacecraft On-Board Computing, thereby achieving reliable spacecraft telecommunication. A spacecraft communication system has inherent capabilities of providing multipoint and broadcast transmission, connectivity between any two distant nodes within a wide-area coverage, quick network configuration /reconfiguration, rapid allocation of space segment capacity, and distance-insensitive cost. To realize the capabilities above mentioned, both the size and cost of the ground-station terminals have to be reduced by using reliable, high-throughput, fast and cost-effective on-board computing system which has been known to be a critical contributor to the overall performance of space mission deployment. Controlled vulnerability of mission data (measured in sensitivity), improved performance (measured in throughput and delay) and fault tolerance (measured in reliability) are some of the most important features of these systems. The system should be thoroughly tested and diagnosed before employing a fault tolerance into the system. Testing and fault tolerance strategies should be driven by accurate performance models (i.e. throughput, delay, reliability and sensitivity) to find an optimal solution in terms of reliability and cost. The modeling and simulation tools will be integrated with a system architecture module, a testing module and a module for fault tolerance all of which interacting through a centered graphical user interface.

Park, Nohpill↗

NASA NTRS1993

Destination-directed, packet-switched architecture for a geostationary communications satellite network

A major goal of the Digital Systems Technology Branch at the NASA Lewis Research Center is to identify and develop critical digital components and technologies that either enable new commercial missions or significantly enhance the performance, cost efficiency, and/or reliability of existing and planned space communications systems. NASA envisions a need for low-data-rate, interactive, direct-to-the-user communications services for data, voice, facsimile, and video conferencing. The network would provide enhanced very-small-aperture terminal (VSAT) communications services and be capable of handling data rates of 64 kbps through 2.048 Mbps in 64-kbps increments. Efforts have concentrated heavily on the space segment; however, the ground segment has been considered concurrently to ensure cost efficiency and realistic operational constraints. The focus of current space segment developments is a flexible, high-throughput, fault-tolerant onboard information-switching processor (ISP) for a geostationary satellite communications network. The Digital Systems Technology Branch is investigating both circuit and packet architectures for the ISP. Destination-directed, packet-switched architectures for geostationary communications satellites are addressed.

Ivancic, William D.↗

NASA NTRS2003

NETMARK: A Schema-less Extension for Relational Databases for Managing Semi-structured Data Dynamically

Object-Relational database management system is an integrated hybrid cooperative approach to combine the best practices of both the relational model utilizing SQL queries and the object-oriented, semantic paradigm for supporting complex data creation. In this paper, a highly scalable, information on demand database framework, called NETMARK, is introduced. NETMARK takes advantages of the Oracle 8i object-relational database using physical addresses data types for very efficient keyword search of records spanning across both context and content. NETMARK was originally developed in early 2000 as a research and development prototype to solve the vast amounts of unstructured and semi-structured documents existing within NASA enterprises. Today, NETMARK is a flexible, high-throughput open database framework for managing, storing, and searching unstructured or semi-structured arbitrary hierarchal models, such as XML and HTML.

Maluf, David A.↗

NASA NTRS2004

Rapid Chemometric Filtering of Spectral Data

A method of rapid, programmable filtering of spectral transmittance, reflectance, or fluorescence data to measure the concentrations of chemical species has been proposed. By programmable is meant that a variety of spectral analyses can readily be performed and modified in software, firmware, and/or electronic hardware, without need to change optical filters or other optical hardware of the associated spectrometers. The method is intended to enable real-time identification of single or multiple target chemical species in applications that involve high-throughput screening of multiple samples. Examples of such applications include (but are not limited to) combinatorial chemistry, flow cytometry, bead assays, testing drugs, remote sensing, and identification of targets. The basic concept of the proposed method is to perform real-time crosscorrelations of a measured spectrum with one or more analytical function(s) of wavelength that could be, for example, the known spectra of target species. Assuming that measured spectral intensities are proportional to concentrations of target species plus background spectral intensities, then after subtraction of background levels, it should be possible to determine target species concentrations from cross-correlation values. Of course, the problem of determining the concentrations is more complex when spectra of different species overlap, but the problem can be solved by use of multiple analytical functions in combination with computational techniques that have been developed previously for analyses of this type. The method is applicable to the design and operation of a spectrometer in which spectrally dispersed light is measured by means of an active-pixel sensor (APS) array. The row or column dimension of such an array is generally chosen to be aligned along the spectral-dispersion dimension, so that each pixel intercepts light in a narrow spectral band centered on a wavelength that is a known function of the pixel position. The proposed method admits of two hardware implementations for computing cross-correlations in real time.

Beaman, Gregory↗

NASA NTRS2009

Life Science Research in Outer Space: New Platform Technologies for Low-Cost, Autonomous Small Satellite Missions

We develop integrated instruments and platforms suitable for economical, frequent space access for autonomous life science experiments and processes in outer space. The technologies represented by three of our recent free-flyer small-satellite missions are the basis of a rapidly growing toolbox of miniaturized biologically/biochemically-oriented instrumentation now enabling a new generation of in-situ space experiments. Autonomous small satellites (~ 1 50 kg) are less expensive to develop and build than fullsize spacecraft and not subject to the comparatively high costs and scheduling challenges of human-tended experimentation on the International Space Station, Space Shuttle, and comparable platforms. A growing number of commercial, government, military, and civilian space launches now carry small secondary science payloads at far lower cost than dedicated missions; the number of opportunities is particularly large for so-called cube-sat and multicube satellites in the 1 10 kg range. The recent explosion in nano-, micro-, and miniature technologies, spanning fields from telecommunications to materials to bio/chemical analysis, enables development of remarkably capable autonomous miniaturized instruments to accomplish remote biological experimentation. High-throughput drug discovery, point-of-care medical diagnostics, and genetic analysis are applications driving rapid progress in autonomous bioanalytical technology. Three of our recent missions exemplify the development of miniaturized analytical payload instrumentation: GeneSat-1 (launched: December 2006), PharmaSat (launched: May 2009), and O/OREOS (organism/organics exposure to orbital stresses; scheduled launch: May 2010). We will highlight the overall architecture and integration of fluidic, optical, sensor, thermal, and electronic technologies and subsystems to support and monitor the growth of microorganisms in culture in these small autonomous space satellites, including real-time tracking of their culture density, gene expression, and metabolic activity while in the space environment. Flight data and results will be presented from GeneSat-1, which tracked gene expression levels of GFP-labeled E. coli and from PharmaSat, which monitored the dose dependency of an antifungal agent against S. cerevisiae. The O/OREOS SESLO instrument, which will study the effects of radiation and microgravity upon the viability and growth characteristics of B. subtilis and the halophile Halorubrum chaoviatoris for periods of 0 - 6 months in space, will be described as well. The ongoing expansion of the small satellite toolbox of biological technologies will be summarized.

Ricco, Antonio J.↗

NASA NTRS2011

Automated Miniaturized Instrument for Space Biology Applications and the Monitoring of the Astronauts Health Onboard the ISS

Human space travelers experience a unique environment that affects homeostasis and physiologic adaptation. The spacecraft environment subjects the traveler to noise, chemical and microbiological contaminants, increased radiation, and variable gravity forces. As humans prepare for long-duration missions to the International Space Station (ISS) and beyond, effective measures must be developed, verified and implemented to ensure mission success. Limited biomedical quantitative capabilities are currently available onboard the ISS. Therefore, the development of versatile instruments to perform space biological analysis and to monitor astronauts' health is needed. We are developing a fully automated, miniaturized system for measuring gene expression on small spacecraft in order to better understand the influence of the space environment on biological systems. This low-cost, low-power, multi-purpose instrument represents a major scientific and technological advancement by providing data on cellular metabolism and regulation. The current system will support growth of microorganisms, extract and purify the RNA, hybridize it to the array, read the expression levels of a large number of genes by microarray analysis, and transmit the measurements to Earth. The system will help discover how bacteria develop resistance to antibiotics and how pathogenic bacteria sometimes increase their virulence in space, facilitating the development of adequate countermeasures to decrease risks associated with human spaceflight. The current stand-alone technology could be used as an integrated platform onboard the ISS to perform similar genetic analyses on any biological systems from the tree of life. Additionally, with some modification the system could be implemented to perform real-time in-situ microbial monitoring of the ISS environment (air, surface and water samples) and the astronaut's microbiome using 16SrRNA microarray technology. Furthermore, the current system can be enhanced substantially by combining it with other technologies for automated, miniaturized, high-throughput biological measurements, such as fast sequencing, protein identification (proteomics) and metabolite profiling (metabolomics). Thus, the system can be integrated with other biomedical instruments in order to support and enhance telemedicine capability onboard ISS. NASA's mission includes sustained investment in critical research leading to effective countermeasures to minimize the risks associated with human spaceflight, and the use of appropriate technology to sustain space exploration at reasonable cost. Our integrated microarray technology is expected to fulfill these two critical requirements and to enable the scientific community to better understand and monitor the effects of the space environment on microorganisms and on the astronaut, in the process leveraging current capabilities and overcoming present limitations.

Human space travelers↗

NASA NTRS1986

Modular, Fast, Two-Dimensional Cyclic Convolver

Proposed high-throughput, real-time synthetic-aperture-radar (SAR) processor built using new, modular, two-dimensional cyclic convolver architecture based on polynomial factorization and designed for very-large-scale integrated (VLSI) circuitry. New architecture reduces cost, size, and power dissipation of SAR processor in comparison to high-speed array-processor approach. Processor also used for other image-and data-processing applications involving two-dimensional Fourier transforms.

Liu, K. Y.↗

NASA NTRS2006

A High-Throughput Processor for Flight Control Research Using Small UAVs

There are numerous autopilot systems that are commercially available for small (<100 lbs) UAVs. However, they all share several key disadvantages for conducting aerodynamic research, chief amongst which is the fact that most utilize older, slower, 8- or 16-bit microcontroller technologies. This paper describes the development and testing of a flight control system (FCS) for small UAV s based on a modern, high throughput, embedded processor. In addition, this FCS platform contains user-configurable hardware resources in the form of a Field Programmable Gate Array (FPGA) that can be used to implement custom, application-specific hardware. This hardware can be used to off-load routine tasks such as sensor data collection, from the FCS processor thereby further increasing the computational throughput of the system.

Klenke, Robert H.↗

NASA NTRS2007

Searching Across the International Space Station Databases

Data access in the enterprise generally requires us to combine data from different sources and different formats. It is advantageous thus to focus on the intersection of the knowledge across sources and domains; keeping irrelevant knowledge around only serves to make the integration more unwieldy and more complicated than necessary. A context search over multiple domain is proposed in this paper to use context sensitive queries to support disciplined manipulation of domain knowledge resources. The objective of a context search is to provide the capability for interrogating many domain knowledge resources, which are largely semantically disjoint. The search supports formally the tasks of selecting, combining, extending, specializing, and modifying components from a diverse set of domains. This paper demonstrates a new paradigm in composition of information for enterprise applications. In particular, it discusses an approach to achieving data integration across multiple sources, in a manner that does not require heavy investment in database and middleware maintenance. This lean approach to integration leads to cost-effectiveness and scalability of data integration with an underlying schemaless object-relational database management system. This highly scalable, information on demand system framework, called NX-Search, which is an implementation of an information system built on NETMARK. NETMARK is a flexible, high-throughput open database integration framework for managing, storing, and searching unstructured or semi-structured arbitrary XML and HTML used widely at the National Aeronautics Space Administration (NASA) and industry.

Maluf, David A.↗

NASA NTRS2006

Adding Hierarchical Objects to Relational Database General-Purpose XML-Based Information Managements

NETMARK is a flexible, high-throughput software system for managing, storing, and rapid searching of unstructured and semi-structured documents. NETMARK transforms such documents from their original highly complex, constantly changing, heterogeneous data formats into well-structured, common data formats in using Hypertext Markup Language (HTML) and/or Extensible Markup Language (XML). The software implements an object-relational database system that combines the best practices of the relational model utilizing Structured Query Language (SQL) with those of the object-oriented, semantic database model for creating complex data. In particular, NETMARK takes advantage of the Oracle 8i object-relational database model using physical-address data types for very efficient keyword searches of records across both context and content. NETMARK also supports multiple international standards such as WEBDAV for drag-and-drop file management and SOAP for integrated information management using Web services. The document-organization and -searching capabilities afforded by NETMARK are likely to make this software attractive for use in disciplines as diverse as science, auditing, and law enforcement.

Lin, Shu-Chun↗